On the interpretation of transcriptome-wide association studies

PLoS Genet. 2023 Sep 7;19(9):e1010921. doi: 10.1371/journal.pgen.1010921. eCollection 2023 Sep.


Transcriptome-wide association studies (TWAS) aim to detect relationships between gene expression and a phenotype, and are commonly used for secondary analysis of genome-wide association study (GWAS) results. Results from TWAS analyses are often interpreted as indicating a genetic relationship between gene expression and a phenotype, but this interpretation is not consistent with the null hypothesis that is evaluated in the traditional TWAS framework. In this study we provide a mathematical outline of this TWAS framework, and elucidate what interpretations are warranted given the null hypothesis it actually tests. We then use both simulations and real data analysis to assess the implications of misinterpreting TWAS results as indicative of a genetic relationship between gene expression and the phenotype. Our simulation results show considerably inflated type 1 error rates for TWAS when interpreted this way, with 41% of significant TWAS associations detected in the real data analysis found to have insufficient statistical evidence to infer such a relationship. This demonstrates that in current implementations, TWAS cannot reliably be used to investigate genetic relationships between gene expression and a phenotype, but that local genetic correlation analysis can serve as a potential alternative.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromosome Mapping
  • Computer Simulation
  • Data Analysis
  • Genome-Wide Association Study*
  • Transcriptome* / genetics

Grants and funding

This work was funded by The Netherlands Organization for Scientific Research (Grant No. NWO VICI 435–14–005 [to DP]) and NWO Gravitation: BRAINSCAPES: A Roadmap from Neurogenetics to Neurobiology (Grant No. 024.004.012 [to DP]), and a European Research Council advanced grant (Grant No, ERC-2018-AdG GWAS2FUNC 834057 [to DP, and funding CdL]). CdL was funded by F. Hoffmann-La Roche AG. WJP was funded by an NWO Veni grant (NWO: 916-19-152). JES was supported by an NWO Veni grant (NWO: 201G-064). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.